[English] 日本語
Yorodumi
- EMDB-61257: Substrate-engaged TIM23 complex from yeast -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-61257
TitleSubstrate-engaged TIM23 complex from yeast
Map data
Sample
  • Complex: Substrate-engaged TIM23 complex from yeast
    • Protein or peptide: Mitochondrial import inner membrane translocase subunit TIM17
    • Protein or peptide: Mitochondrial import inner membrane translocase subunit TIM23
    • Protein or peptide: Mitochondrial import inner membrane translocase subunit TIM44,L-lactate dehydrogenase (cytochrome),sfGFP
    • Protein or peptide: Protein MGR2
    • Protein or peptide: anti-Tim44-Fab H chain
    • Protein or peptide: anti-Tim44-Fab L chain
    • Protein or peptide: Substrate
  • Ligand: CARDIOLIPIN
KeywordsMitochondrial protein import / TOM / TIM23 protein translocation / PROTEIN TRANSPORT
Function / homology
Function and homology information


PAM complex, Tim23 associated import motor / L-lactate dehydrogenase (cytochrome) / L-lactate dehydrogenase (cytochrome) activity / extrinsic component of mitochondrial inner membrane / Mitochondrial protein import / TIM23 mitochondrial import inner membrane translocase complex / mitochondrion targeting sequence binding / protein insertion into mitochondrial inner membrane / lactate metabolic process / protein import into mitochondrial matrix ...PAM complex, Tim23 associated import motor / L-lactate dehydrogenase (cytochrome) / L-lactate dehydrogenase (cytochrome) activity / extrinsic component of mitochondrial inner membrane / Mitochondrial protein import / TIM23 mitochondrial import inner membrane translocase complex / mitochondrion targeting sequence binding / protein insertion into mitochondrial inner membrane / lactate metabolic process / protein import into mitochondrial matrix / transmembrane protein transporter activity / intracellular protein transport / mitochondrial intermembrane space / protein-folding chaperone binding / protein-macromolecule adaptor activity / mitochondrial inner membrane / heme binding / mitochondrion / ATP binding / metal ion binding / nucleus / cytosol
Similarity search - Function
Romo1/Mgr2 / Reactive mitochondrial oxygen species modulator 1 / Reactive mitochondrial oxygen species modulator 1 / Mitochondrial inner membrane translocase complex, subunit Tim17 / Mitochondrial inner membrane translocase complex, subunit Tim23 / Tim23-like / Mitochondrial import inner membrane translocase subunit Tim44 / Tim44-like / L-mandelate/L-lactate dehydrogenase, FMN-binding domain / Cytochrome b5, heme-binding site ...Romo1/Mgr2 / Reactive mitochondrial oxygen species modulator 1 / Reactive mitochondrial oxygen species modulator 1 / Mitochondrial inner membrane translocase complex, subunit Tim17 / Mitochondrial inner membrane translocase complex, subunit Tim23 / Tim23-like / Mitochondrial import inner membrane translocase subunit Tim44 / Tim44-like / L-mandelate/L-lactate dehydrogenase, FMN-binding domain / Cytochrome b5, heme-binding site / Cytochrome b5 family, heme-binding domain signature. / FMN-dependent alpha-hydroxy acid dehydrogenase, active site / FMN hydroxy acid dehydrogenase domain / FMN-dependent alpha-hydroxy acid dehydrogenases active site. / FMN-dependent alpha-hydroxy acid dehydrogenase domain profile. / Cytochrome b5 family, heme-binding domain profile. / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5-like heme/steroid binding domain superfamily / Cytochrome b5-like Heme/Steroid binding domain / Cytochrome b5-like Heme/Steroid binding domain / FMN-dependent dehydrogenase / FMN-dependent dehydrogenase / Tim44-like domain / Tim44-like domain / Tim44 / Tim17/Tim22/Tim23/Pmp24 family / NTF2-like domain superfamily / Aldolase-type TIM barrel
Similarity search - Domain/homology
L-lactate dehydrogenase (cytochrome) / Mitochondrial import inner membrane translocase subunit TIM23 / Mitochondrial import inner membrane translocase subunit TIM17 / Mitochondrial import inner membrane translocase subunit TIM44 / Protein MGR2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Saccharomyces cerevisiae S288C (yeast) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.83 Å
AuthorsYang YQ / Wang GP / Wang SS
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271269 China
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Dynamic TOM-TIM23 supercomplex directs mitochondrial protein translocation and sorting.
Authors: Yuqi Yang / Shanshan Wang / Guopeng Wang / Yuke Lian / Lingfeng Xue / Wenhong Jiang / Qiang Guo / Chen Song / Long Li /
Abstract: The mitochondrial translocase of the outer membrane (TOM) and translocase of the inner membrane 23 (TIM23) complexes are coupled to control protein import across the outer and inner membranes, ...The mitochondrial translocase of the outer membrane (TOM) and translocase of the inner membrane 23 (TIM23) complexes are coupled to control protein import across the outer and inner membranes, respectively. However, the mechanisms of protein recognition and sorting in the TOM-TIM23 pathway remain unclear. Here we report cryo-electron microscopy structures of a translocating polypeptide substrate captured in the active TOM-TIM23 supercomplex from Saccharomyces cerevisiae. In the TOM complex, the polypeptide substrate adopts multiple conformations stabilized by hydrophilic residues from distinct regions of the Tom40 channel. In the TIM23 complex, the Tim17 and Mgr2 subunits create the translocation pathway, with a central restriction formed by four highly conserved hydrophobic residues. The substrate primarily interacts with hydrophobic residues along the Tim17-Mgr2 pathway. Substrate hydrophobicity modulates the association of Mgr2 with Tim17, enabling dynamic regulation of protein sorting toward either the matrix or membrane. These findings reveal a sophisticated translocation mechanism of the TOM-TIM23 supercomplex that ensures the efficient import of diverse mitochondrial proteins.
History
DepositionAug 22, 2024-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_61257.png

Downloads & links

-
Map

FileDownload / File: emd_61257.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 300 pix.
= 285. Å		0.95 Å/pix.
x 300 pix.
= 285. Å		0.95 Å/pix.
x 300 pix.
= 285. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.44
Minimum - Maximum-1.3860798 - 2.1961918
Average (Standard dev.)0.0025949138 (±0.04197791)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 285.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_61257_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_61257_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Substrate-engaged TIM23 complex from yeast

EntireName: Substrate-engaged TIM23 complex from yeast
Components
  • Complex: Substrate-engaged TIM23 complex from yeast
    • Protein or peptide: Mitochondrial import inner membrane translocase subunit TIM17
    • Protein or peptide: Mitochondrial import inner membrane translocase subunit TIM23
    • Protein or peptide: Mitochondrial import inner membrane translocase subunit TIM44,L-lactate dehydrogenase (cytochrome),sfGFP
    • Protein or peptide: Protein MGR2
    • Protein or peptide: anti-Tim44-Fab H chain
    • Protein or peptide: anti-Tim44-Fab L chain
    • Protein or peptide: Substrate
  • Ligand: CARDIOLIPIN

-
Supramolecule #1: Substrate-engaged TIM23 complex from yeast

SupramoleculeName: Substrate-engaged TIM23 complex from yeast / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

-
Macromolecule #1: Mitochondrial import inner membrane translocase subunit TIM17

MacromoleculeName: Mitochondrial import inner membrane translocase subunit TIM17
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 16.602156 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MSADHSRDPC PIVILNDFGG AFAMGAIGGV VWHGIKGFRN SPLGERGSGA MSAIKARAPV LGGNFGVWGG LFSTFDCAVK AVRKREDPW NAIIAGFFTG GALAVRGGWR HTRNSSITCA CLLGVIEGVG LMFQRYAAWQ AKPMAPPLPE APSSQPLQA

UniProtKB: Mitochondrial import inner membrane translocase subunit TIM17

-
Macromolecule #2: Mitochondrial import inner membrane translocase subunit TIM23

MacromoleculeName: Mitochondrial import inner membrane translocase subunit TIM23
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 23.266527 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSWLFGDKTP TDDANAAVGG QDTTKPKELS LKQSLGFEPN INNIISGPGG MHVDTARLHP LAGLDKGVEY LDLEEEQLSS LEGSQGLIP SRGWTDDLCY GTGAVYLLGL GIGGFSGMMQ GLQNIPPNSP GKLQLNTVLN HITKRGPFLG NNAGILALSY N IINSTIDA ...String:
MSWLFGDKTP TDDANAAVGG QDTTKPKELS LKQSLGFEPN INNIISGPGG MHVDTARLHP LAGLDKGVEY LDLEEEQLSS LEGSQGLIP SRGWTDDLCY GTGAVYLLGL GIGGFSGMMQ GLQNIPPNSP GKLQLNTVLN HITKRGPFLG NNAGILALSY N IINSTIDA LRGKHDTAGS IGAGALTGAL FKSSKGLKPM GYSSAMVAAA CAVWCSVKKR LLEK

UniProtKB: Mitochondrial import inner membrane translocase subunit TIM23

-
Macromolecule #3: Mitochondrial import inner membrane translocase subunit TIM44,L-l...

MacromoleculeName: Mitochondrial import inner membrane translocase subunit TIM44,L-lactate dehydrogenase (cytochrome),sfGFP
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: L-lactate dehydrogenase (cytochrome)
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 84.451133 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MHRSTFIRTS GTSSRTLTAR YRSQYTGLLV ARVLFSTSTT RAQGGNPRSP LQIFRDTFKK EWEKSQELQE NIKTLQDASG KLGESEAYK KAREAYLKAQ RGSTIVGKTL KKTGETMEHI ATKAWESELG KNTRKAAAAT AKKLDESFEP VRQTKIYKEV S EVIDDGES ...String:
MHRSTFIRTS GTSSRTLTAR YRSQYTGLLV ARVLFSTSTT RAQGGNPRSP LQIFRDTFKK EWEKSQELQE NIKTLQDASG KLGESEAYK KAREAYLKAQ RGSTIVGKTL KKTGETMEHI ATKAWESELG KNTRKAAAAT AKKLDESFEP VRQTKIYKEV S EVIDDGES SRYGGFITKE QRRLKRERDL ASGKRHRAVK SNEDAGTAVV ATNIESKESF GKKVEDFKEK TVVGRSIQSL KN KLWDESE NPLIVVMRKI TNKVGGFFAE TESSRVYSQF KLMDPTFSNE SFTRHLREYI VPEILEAYVK GDVKVLKKWF SEA PFNVYA AQQKIFKEQD VYADGRILDI RGVEIVSAKL LAPQDIPVLV VGCRAQEINL YRKKKTGEIA AGDEANILMS SYAM VFTRD PEQIDDDETE GWKILEFVRG GSRQFTPNHP GGQDVIKFNA GKDVTAIFEP LHAPNVIDKY IAPEKKLGPL QGSGS GSKG EELFTGVVPI LVELDGDVNG HKFSVRGEGE GDATNGKLTL KFICTTGKLP VPWPTLVTTL TYGVQCFSRY PDHMKR HDF FKSAMPEGYV QERTISFKDD GTYKTRAEVK FEGDTLVNRI ELKGIDFKED GNILGHKLEY NFNSHNVYIT ADKQKNG IK ANFKIRHNVE DGSVQLADHY QQNTPIGDGP VLLPDNHYLS TQSVLSKDPN EKRDHMVLLE FVTAAGITHG SAGLEVLF Q GPANGGSAWS HPQFEKGGGS GGGSGGGSWS HPQFEK

UniProtKB: Mitochondrial import inner membrane translocase subunit TIM44, L-lactate dehydrogenase (cytochrome)

-
Macromolecule #4: Protein MGR2

MacromoleculeName: Protein MGR2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 12.264158 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MPPLPQNYAQ QQPSNWDKFK MGLMMGTTVG VCTGILFGGF AIATQGPGPD GVVRTLGKYI AGSAGTFGLF MSIGSIIRSD SESSPMSHP NLNLQQQARL EMWKLRAKYG IRKD

UniProtKB: Protein MGR2

-
Macromolecule #5: anti-Tim44-Fab H chain

MacromoleculeName: anti-Tim44-Fab H chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 25.635932 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MDWTWRVFCL LAVAPGAHSQ VQLKQSGPGL VQPSQSLSIT CTVSGFSLTT YGVHWVRQSP GKGLEWLGVM WRGGSTDFNA AFMSRLSIT KDNSKSQVFF KMNSLQADDT AIYYCARYGN YDAMDYWGQG TSVTVSSAKT TPPSVYPLAP GSAAQTNSMV T LGCLVKGY ...String:
MDWTWRVFCL LAVAPGAHSQ VQLKQSGPGL VQPSQSLSIT CTVSGFSLTT YGVHWVRQSP GKGLEWLGVM WRGGSTDFNA AFMSRLSIT KDNSKSQVFF KMNSLQADDT AIYYCARYGN YDAMDYWGQG TSVTVSSAKT TPPSVYPLAP GSAAQTNSMV T LGCLVKGY FPEPVTVTWN SGSLSSGVHT FPAVLQSDLY TLSSSVTVPS SPRPSETVTC NVAHPASSTK VDKKIVPRDC

-
Macromolecule #6: anti-Tim44-Fab L chain

MacromoleculeName: anti-Tim44-Fab L chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 26.14015 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MVLQTQVFIS LLLWISGAYG DIVLTQSPAS LAVSLGQRAT ISCRASESVD IYGISFMNWF QQKPGQPPKL LIYATSNQGS GVPARFSGS GSGTDFSLNI HPMEEDDTAM YFCQQSKEVP RTFGGGTKLE IKRADAAPTV SIFPPSSEQL TSGGASVVCF L NNFYPKDI ...String:
MVLQTQVFIS LLLWISGAYG DIVLTQSPAS LAVSLGQRAT ISCRASESVD IYGISFMNWF QQKPGQPPKL LIYATSNQGS GVPARFSGS GSGTDFSLNI HPMEEDDTAM YFCQQSKEVP RTFGGGTKLE IKRADAAPTV SIFPPSSEQL TSGGASVVCF L NNFYPKDI NVKWKIDGSE RQNGVLNSWT DQDSKDSTYS MSSTLTLTKD EYERHNSYTC EATHKTSTSP IVKSFNRNEC

-
Macromolecule #7: Substrate

MacromoleculeName: Substrate / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 1.294587 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)

-
Macromolecule #8: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 8 / Number of copies: 1 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 160770
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more